Israeli nationalists shouted "death to the Arabs", "may your villages burn" and "Gaza is a graveyard" during a government-supported procession through Jerusalem marking the anniversary of the city's seizure and annexation.

This yearly display of Jewish authority over Palestinian East Jerusalem has become increasingly radical in recent years, with Thursday's gathering reaching a peak as National Security Minister Itamar Ben-Gvir raised an Israeli flag in front of the al-Aqsa mosque, the most sacred Islamic site in the city.

Most Palestinians in the Old City's Muslim quarter had closed their shops and left before the march started, but far-right Jewish extremists who slipped in clashed with remaining residents, hurling chairs at each other until police, arriving in large numbers that afternoon, separated them.

"I've come to show the entire world that this is our city, the Holy Land. God gave us this land and this city," said Ariel Amichai, a 19-year-old marcher.

Questioned on the march's message to Jerusalem's Palestinians, he answered: "That they must go. This is our country. They can't just stay here and try to stab or kill us."

Amichai, from Modi'in 43km from Jerusalem, believed Jerusalem Day - commemorating the 1967 capture of the city's east side - was the only time Jews could enter the Muslim quarter via Damascus Gate, even though Israeli Jews and Palestinians pass through it daily.

Marchers arrived by bus from across Israel and occupied West Bank settlements in a massive operation funded by the Jerusalem municipality and government ministries. Finance Minister Bezalel Smotrich also participated in Thursday's event.

With Palestinians gone from the Old City, much of the friction shifted to clashes between the official marchers and members of Standing Together, a Jewish group there to shield Palestinian residents from political violence.

Suf Patishi, an organizer with Standing Together, said a record 400 volunteers showed up in the group's signature purple hi-vis vests on this high-risk day.

"We wanted to cover every corner of the city to ensure we stopped attacks on Palestinians," Patishi said. "Yes, it's dangerous for us, but nothing compared to the danger faced by Palestinians living here."

A handful of religious Jews joined the protective line of counter-protesters. An ultra-orthodox man in a long grey beard and gold coat, who came from northern Israel and gave only his name as David, was among them.

"I've grown appalled by the violent conduct of people in my community," David said. "I'm a man of faith, religious, and they're acting in our name. This desecrates God's name, so the remedy is to do the opposite - a Kiddush Hashem, a sanctification of God's name."

At the al-Aqsa compound, known to Jews as the Temple Mount, Ben-Gvir danced with supporters chanting "the Temple Mount is in our hands" as he unfurled an Israeli flag. The national security minister has spearheaded efforts to challenge the 59-year status quo - in place since Israel's 1967 capture of East Jerusalem and the West Bank - that bars non-Muslims from praying in the holy area.

On Thursday evening, Ben-Gvir posted on his Telegram account: "59 years after the liberation of Jerusalem, I raised the Israeli flag on the Temple Mount and we can proudly say: We have returned governance to the Temple Mount."